AUIII Transmission Slipping?

[Timeshift]

Hi Guys,
I have an AUIII, pic on the left, manufactured 04/2002 and has done 59,000k. A few thousand km ago, I had a problem with the transmission where it was not as smooth as it should be on 2-3. They found some sort of cracked bolt or screw and replaced it, but as a result, my transmission fluid was completely burnt and they advised it would be $250 to drain and replace (really, it was a result of the bolt so I think it should be under warranty..) and that I should wait no longer than my next service which is scheduled for June.

Today when I went to drive, for the first time ever, my car would not start on ignition - no cranking at all. Moved the trans from Park down to 1 and back again, and it started. Later on when I started up my car again, i placed it in to drive, but when I went to accellerate, it acted like it was in neutral and kicked in to drive after a brief second of revving. Again it did this at a traffic light a few minutes later. It also acted like it was in neutral during what I believe was a 1-2 shift, but could have been 2-3.

Is this likely to be a result of the burnt transmission fluid? Ultra tune quote me a price of $150, but would this invalidate the half a month of warranty I have left, which I may need if replacing it does not assist in solving the problem? Is this issue likely to simply be resolved with trans fluid replacement or does it sound like something deeper, maybe the transmission itself? Is the transmission covered under warranty if it has been subjected to burnt fluid, despite being caused by an issue fixed under warranty anyway?

Thoughts and comments appreciated :1syellow1